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Abstract

Over the last decade, the emergence of high-throughput sequencing has led to an increase in both the size and scope of genome sequencing projects. Although genome sequencing and analysis has changed dramatically during this time, the way read alignments are visualised has remained largely unchanged. To address the problem of visualising growing sequencing datasets, we have developed DiscoPlot, a tool for visualising read alignments using a two-dimensional scatterplot. DiscoPlot allows the user to quickly identify genomic rearrangements, misassemblies and sequencing artefacts by providing a scalable method for visualising large sections of the genome. It reads single-end or paired read alignments in SAM, BAM or standard BLAST tab format and creates a scatter plot of opaque crosses representing the alignments to a reference. DiscoPlot is freely available (under a GPL license) for download (Mac OS X, Unix and Windows) at https://mjsull.github.io/DiscoPlot.

Author Comment

This is Version 1 of the manuscript, formatted for PeerJ Submission.

Additional Information

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Mitchell J Sullivan conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables.

Scott A Beatson conceived and designed the experiments, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

ENA - ERR687901

Data Deposition

The following information was supplied regarding the deposition of related data:

http://mjsull.github.io/DiscoPlot

Funding

SAB is supported by a Career Development Fellowship from the National Health and Medical Research Council Career of Australia [grant number APP1090456]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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